Personally, I was never fond of Manga Studio. I found that it gave the comic too much of a stark, digital look. The lines are too crisp. It's a matter of taste that determined my opinion, but I rather much liked the softer brush feel and freedom of Photoshop. Granted, MS has features such as screentones and perspective lines that Photoshop (the one I'm using) has not, and I need to install those features separately.
I think the best looking comics still come from traditional work either way. But that's obviously an expensive alternative that not many can afford.
I think MS is helpful in that it has all the basics and features preset for a comic, whereas Photoshop can be treated more like a canvas with more liberty on the set up. I find the free-hand techniques much more appealing. Drawing your own panels, speech bubbles and sound effects goes a very long way!
And of course, Photoshop is much more capable with colours 